(posted in Evolution)

To my mind it makes no difference what the personal beliefs of a scientist are, as long as the focus of their professional career is to do excellent science. Denial of one aspect of science in supplication to some other philosophy or faith is always a bad move if you want to be taken seriously as a scientist. There are plenty of excellent scientists who are also religious, but I would say that very few of them are serious biologists who don't accept evolution. Like David said, the evidence in favour of evolution is many, varied and vast, to the point of being nearly incontrovertible. Evolution theory is so powerful as an explanatory tool that to deny it's validity would require rejection of virtually all other science and dismissal of reason as a good way of thinking about things.

This is definitely a grey area, where the divide between biology and chemistry is shown to be a less-than-clear fuzzy line. Yes, a virus in isolation cannot replicate, but to some degree all living things are dependant on some critical biotic or abiotic factor, without which they cannot survive. So a virus needs a host cell but that host cell in turn needs, for example, a correct temperature range or specific types of nutrients to be available. Parasites are often helpless without their host organism.

I tend to think of viruses as a kind of inbetween state, off-shoots or perhaps contemporaries of the cell-based DNA and RNA replicators that were our ancestors. But while our ancestors explored genetic and phenotypic complexity, the proto-viriods were selected to parasitise those developing pathways, to take advantage of them without having to discover or maintain the genes. Not quite alive, but definitely biochemistry.

So just to be clear, you are transforming some ecoli, then purifying DNA from a colony?

If this is the case, then no, the quality of the transformed DNA won't have an impact. The degree of supercoiled etc in a plasmid prep is dependant on the plasmid itself and what kind of cells you are using.

(posted in Mammals)

Not that I've ever heard of. The joints in legs are highly conserved across the wide taxon tetrapoda, which includes mammals.

Not every trait requires a specific adaptive advantage. I can't sepcifically comment on the polecat's bandit mask, but random genetic drift and sexual selection can account for superficial changes like this.

We do no know how to bring people back to life. Sometimes we can restart a person's heart without them dying, if we get to them fast enough, but they didn't really die.

First off, evolution "as Darwin suggests" is wrong in many way. For example, he didn't know about DNA and advocated panspermia as a distribution method. The modern synthesis of evolutionary theory says that two species comes from one which split and evolved separately for long enough to be reproductively isolated. This can result in minor changes over short time scales, like a few feather colours, or drastic changes over long time scales, such as aquatic to terrestrial living. All changes are random, but which survives is not, so one population of birds could  lose or acquire blue tinted feathers, the other remain the same as the ancestral colouration, all through the action of random mutation events followed by non-random selection.

(posted in General Biology)

Could be a dried piece of a sea star, but I'm not sure.

Those certainly look like strawberry leafs to me. The "onion" might be onion grass, which is edible.

(posted in Mammals)

They are very real on the Discworld....

http://tvtropes.org/pmwiki/pmwiki.php/M … pBearsOhMy

Drop Bears are large, carnivorous creatures closely related to koala "bears". They hunt prey by climbing tall trees and then ambushing them from above. Certain techniques can be used to deter drop bears, such as smearing Vegemite behind one's ears. The drop bear does not have any reported sightings or basis in folklore, and the myth was basically created to scare tourists in Australia. Interestingly, however, the drop bear has an extrordinary resemblance to a now-extinct creature known as Thylacoleo or the marsupial lion — a prehistoric, tree-dwelling ambush predator whose closest known relatives are wombats and koalas. However, this is obviously just an eerie coincidence.

Well, this is an issue of semantics. The cladist view of bird phyologeny puts them firmly in the dinosaur clade, which basically makes all birds feathered dinosaurs. Scientists often talk about dinosaurs with "non-avian" as a qualifying suffix to exclude modern birds when talking about the extinct reptiles. A differing view that is the Linnean taxonomy, where birds are given their own catagory separate from dinosaurs.

Basically there is a very fuzzy line between modern birds and non-avian dinosaurs, which makes the dinstinction hard to pin point.

Kind of, though I wouldn't use the term evolve. DNA doesn't evolve, populations evolve. DNA mutates. Evolution means mutation AND selection.

But, recently there was a study published that looked at colary restriction and found that where people faced significant hardship (ie not enough food) their children and grandchildren benefited from significantly lower levels of heart disease. It is though that this effect is due to epigenetic effects, where gene regulation is altered in a heritable way without actual DNA sequence changes. You can view epigenetic changes as a form of mutation, because it does permanently alter the phenotype of an individual in a heritable manner, but is far more subtle and controlled than a random nucleotide change.

(posted in Mammals)

I'd say your best bet is an insect, even if it is too early. The behaviour of falling silent when you approach closely sounds very like when I hunt for cicadas. It could also be a bird, sitting on the ground. I don't know of any mammals that make insect-like sustained chirping noises. Do you get frogs in Finland? Some frog calls can easily be mistaken for insect or bird calls.

The definition of a vestigial organ is one which has lost its original function. This does in no way preclude adaptation of the organ to a new purpose. In humans the appendix is usually touted as a vestigial organ, but it certainly has a purpose (gut flora reservoir, with immume sensitivity implications). Our limbs were themselves vestigal at one point, as they were no longer used for swimming by our tetrapod ancestors. Definitely not a dead end!

The reason they have two horns is because of bilateral symmetry, just like having two eyes or two arms. There are all kinds of different horns, such as antlers, and they are typically used for mating fights, as well as defense. Fights of this kind can get vicious, and it isn't limited to horned herbivores. Male lions fight and they have much deadlier accessories, but mostly they don't kill or even seriously injure one another. This is partially behavioural, which is also the case with horned mammals when they fight; the loser is allowed to retreat without extensive pursuit. I can't speak about the angle of horns specifically, but it does make sense for evolution to limit injuries in mating fights.


(posted in Genes, Genetics and DNA)

Differentiating facial features is fairly difficult primarily because it requires detection of sometimes quite subtle differences. We are attuned to these differences, and are quite good at telling human faces apart, but what seems to happen is that our brains are calibrated to recognise faces in our society. As soon as you go far enough outside the averages of that society, the "calibrations" go out of whack and you might find it much more difficult to distinguish between peoples who belong to a different ethnic group than the one you grew up amongst. It's a little like a language; identifying subtleties in a language you know is easy, but an unfamiliar language is much more challenging, especially when it uses sounds that our ear is not attuned to.

It should also be noted that some animals use different senses from vision to detect individuals. Smell and sound are also very important, smell especially amongst rodents. There is also the possibility of colouration that humans cant' see. Insects and birds have vision outside of our visible range, into the UV spectrum. This is illustrated very well in flowers which might look simply white to us, but from the point of view of the insect or bird they have UV-range bright patterns.

(posted in Research and Careers)

It is very common for researchers to take jobs all over the world. For example, right now I'm looking at naturejobs website and I see jobs in the USA, Canada, much of Europe, China, South America, Australia....pretty much all over the world, and that is already filtered for the kinds of jobs I might do:)

Also no an expert, but this (rather awesome) video on youtube seems to show the chameleon changing colour to respond to environment colour.


A quick bit of reading implies that the exact reason a chameleon alters it's colouration is down to which chameleon you are talking about. Some do use it for thermoregulation, particularly desert species, some use it for mating, and some for camouflage. There are aspect of reflex (like, change to a default camouflage colour when threatened) and some which are informed by environment (see the video above). I couldn't discover exactly how the animal "decides" to change to which colour, but I suspect they simply use their eyes to see, which is then processed into skin colour.

Edit: OK, so the video is a fake. That's egg on my face.

Hi Jason.

A chaperonin is actually a pretty broad catagory. It is used to describe all different kinds of proteins which have an influence on protein folding. For example, the GroES/L system is a large chaperonin complex. This complex forms a chamber which allows a protein to fold correctly.


There is another type which simply binds to sensitive hydrophobic regions of a polypeptide as it is synthesised, protecting it until it is finished and can fold properly. An example of these are the DnaJ/K system.


Yet another type helps proteins with their folding chemistry by masking their free cysteines until they can form properly arranged disulfide bonds.


Not all proteins need chaperones to fold correctly, and many protein can be denatured completely then spontaneously re-fold, all outside of a cell and without any folding machinery. Chaperonins are much more important when an organism is under stress, like non-optimal pH or too high a temperature. Many of these chaperonins are called heat shock proteins because they are upregulated during times of thermal stress to help more sensitive proteins fold, thus keeping the organism viable outside of its normal temperature range.

The comparison between rodents and kangaroo is not really a good one. These animals are from two different clades of mammals; the Placentals (bears, wolves, and all of the others you mentioned) and marsupials (kangaroo, Tasmanian devils, koala, wombats, possums). There is another major clade, monotremata, which includes egg-laying mammals, such as platypus and echidna.


All of these groups are mammals, in that they have fur and produce milk to feed their young. But, in terms of their reproduction, they vary in one very important innovation; Placental mammals, as their name suggests, have placentas. This is a highly specialised organ that allows a mother to feed an embryo internally by bringing her blood supply in very close proximity to that of the embryo's, facilitating direct nutrient exchange and allowing development to proceed at full pace. In contrast, marsupials and monotremes have no such structure. Consequently, for non-placental mammals feeding the embryo in utero beyond a certain size point becomes a major issue.


Marsupials dealt with this problem by giving birth very early in development and using their pouches, which provide shelter for the new born and give direct access to food via mammaries in the pouch. Monotremes get around the same problem the same way birds do, by laying eggs which contain all of the nutrients (the egg yolk) needed for the embryo to develop properly until it is ready to hatch.

There are other ecological factors that influence young size. For example, if you compare something like an antelope to a monkey, the antelope is far more developed and can run with the herd, whereas the baby monkey is comparatively small and helpless. But the differences between reproduction methods in different mammal clades can account for the extreme examples you mentioned.

Jonathan is quite right, biology is such a broad subject area, there really isn't any one answer, apart from "life".

I often struggle to put myself into a biology box, and usually have to use a few different words, which may even change from project to project. If I were pinned down, I say that I study protein biochemistry, with aspects of microbiology, molecular genetics and evolution, though the last one can easily be applied to virtually all biology!

It depends. Translation can controlled by various factors , including alternative splicing, RNA secondary structure or the poly-A tail. For example, if one of the introns contains a stop codon you won't get complete transcription if it were done before splicing. It's the same situation after insertion into a prokaryote, although the translational controls are different in prokaryotes. Transgenic expression of a eukaryotic gene in prokaryote is usually started from cDNA to remove the introns and inserted in a dedicated microbial expression vector designed to produce the transcript in a form usable by the host cell.

The over riding factor is gamete production. If it produces sperm, it is male. If it produces ova (egg cells), it is female. Some animals and plants produce both, and so are termed hermaphrodite.

One important implication of what Reetika mentions is that when looking at more distantly related genes, the nucleotide sequence has generally diverged much more then the amino acid sequence, due to redundancy in the genetic code. So, amino acid sequence can give you a more easily interpretable result than the nucleotides alone, enabling you detect similarity at a further evolutionary remove.

That being said, nucleotide sequence alignment can be more useful in much more closely related sequences, where (for example) you are looking at random nucleotide changes to determine a pattern of relatedness where the changes are inherited, but don't necessarily equate to phenotype (ie protein) changes.

I'm just guessing, but I think those might be seeds. See if you can smash one open, you might be able to identify en ambryo with different layers, if it is a seed. If they are teeth, they will be basically solid.

The consensus is a little murky, but broadly, homosexuality isn't strictly genetic, rather it is more accurately described as developmental. Even twins in utero develop slightly differently after the embryo splits; getting slightly different levels of nutrients for example. Also, sexual preference is a continuum not a binary, and is influenced a bit by social cues, making it even more fuzzy. I personally know twin brothers, one of whom is gay, the other, straight. What it boils down to is that sexual orientation is not a straight (haha) forward genetic trait, but a complex trait influenced by multiple environmental factors during embryonic development.

(posted in General Biology)

Agreed, a very ambiguous question.

(posted in Evolution)

Derek said;

"It must vary according to the need of the different species which leads me to the conclusion that evolution is by design and not random."

First off, there is no "must" or "need". It is more correct to describe it thus: Biochemical processes (and by extension, physical traits) are shaped by the interplay between the organism within which they happen and the environment the organism finds itself in. Those biochemical processes (for example, fear of a tiger, or attachment to one's offspring, or stripes as camouflage, or herding instinct, or long legs good for running...the list goes on) which promote survival of an organism tend, over generations, to increase in frequency in a population. Occasionally genetic innovation gives rise to new traits, and occasionally old traits are lost. Occasionally one species becomes two, and occasionally one species dies out. There is no "must" or "need", just "is".

You are setting up design and randomness in a false dichotomy. Evolution produces things that look designed, but are the product of many intersecting blind forces, some of which are random, most of which are definitely not. These forces are universally fundamental and not biological, such as osmosis and diffusion, pressure, temperature, chemistry of all kinds and other physical equilibria. Emergent from those abiotic forces is the complex dynamics found in biology, which is where evolution happens.

I'm afraid that the way you are using "dormancy" is not a defined term, any more then the other one you came up with, "induced stimulation", so I can't comment on that. Perhaps you should learn more about biology in general, and evolution in particular, then reformulate your question.

Inferring design because you don't understand evolution or biochemistry is not a viable argument (the logic term is argument from ignorance) either against evolution or for design. This fixation on emotion is a little strange; as I said, emotion is a biochemical process like any other, and can be selected and evolved, like any other.

I'm afraid that "knowing" is the wrong word. Virus particles are in the grey area between animate and inanimate, though they have genes and are very much subjected to evolution which for my money makes them alive. They don't "know", they are, like all living things, self sustaining biochemical reactions. Thus, when a virus enters a cell, or a bacteria replicates, it does so not because it chooses to but because that is what its biochemistry has evolved to do to survive.

(posted in Evolution)

Emotion is a biophysical process, available for selection like any other biophysical process. Love is adaptive because it enhances protection of offspring or mates. Fear is adaptive because it enhances survival in dangerous circumstances, like when under predation or other physical threat. These and other basic emotions we seem to share with many animals, and separating them out in humans as if they were somehow not part of evolution is a distinction without a difference.

Anything is possible, but "design" is not a necessary part of evolutionary hypotheses. There are elements of randomness in evolution, most notably in the origin of mutations. But, natural selection is very much non-random. It does result in things which appear to be designed but are actually adapted by the complex interplay between genome and environment. Hence, design is not a necessary element to introduce in order to make a complete explanation of evolution. I'm using the term environment in the broadest possible sense here, which includes not just weather and geography, but pretty much every factor at play above the gene sequence level; chromosomal structure, protein transcription rates, enzyme efficiencies, cell-cell interactions, inter- and intraspecific dynamics, ecosystem level dynamics: everything.

I'm afraid that I don't know what you mean by "induced stimulation". Perhaps a similar concept is drift, where essentially random events, like a tree falling on you, being caught in a landslide or missing our on mating because there weren't enough mates to go around (basically any slight statistical bias that isn't directly linked to phenotype), have an appreciable effect on diversity without there being a positive or negative selective pressure to drive it.

I'm afraid that very little is known for certain about the evolution of intelligence, but diversity is the currency for ALL evolutionary changes, not just intelligence. My personal view is that intelligence is a successful adaptive strategy, and that if evolution were re-run from the beginning it would probably arise again, just like many other traits, e.g. eyes. But to take that a step further and say that intelligence was somehow pre-destined, that is just supposition.

This is really something that you should talk to your advisor about. From memory, the conversion kit comes with different reading frame options, so you just need to work out what the correct frame for you is and select the one which compensates correctly.

There are virtual BP/LR reaction you can do to test out your constructs if you get stuck; I have used Geneious in the past for modifying my own vectors.

Speaking from an evolutionary perspective, proteins essential to the setup you see in extant organisms were not always essential. It is thought that RNA was the primary material that enzymes were made of, called ribozymes. For example, the ribosome is basically a huge ribozyme, made up of several large RNA molecules, along with some accessory proteins. Also, protein synthesis is mediated by RNA carrier molecules called tRNAs.

Basically put, protein synthesis must have originally been first performed exclusively with ribozymes, and proteins were later incorporated as useful sequences were discovered by evolution.

There is an inescapable logic to abiogenesis. We know that there is life now, and according to our best science, at one point there probably wasn't any life. Therefore, life must have come from non-life, hence abiogenesis. Even if you speculate that Earth was seeded from elsewhere, the question is only deferred to how life began elsewhere.

No one really has a clear idea how this happened, but there are a few hypotheses.

Have a look at this one:

It's hard to say, but I suspect wary interest or fear from the domestic cat and more or less indifference from the lion. It would heavily depend on previous exposure and experience.

(posted in Genes, Genetics and DNA)

In a very general sense, structural features in a 3D shape like tRNA may not have a "direct" biological function, but simply may be there to support the parts which do have a direct function. This support might be in the form of: keeping two parts physically separate, providing regulatory elements or maybe contributing to the free energy of folding to ensure proper presentation of the biochemically active bits. These are only general concepts in biological macromolecules. Like Reetika says, we don't really know what every part of tRNA molecules do.

Yikes, that is a loaded question. First off, to be a "christian" is a very widely varied thing, with lots and LOTS of different views on different kinds of science.

The prerequisites of being a scientist are to have an open inquiring mind, a willingness to learn and work hard and the capacity to question critically. While that may seem diametrically opposed to many brands of christianity, religious people all over the world can and do become excellent scientists. The explanation I've usually heard is that whatever critical thinking skills they might develop simply aren't applied to the articles of their faith.

Amoungst people with higher degrees in science there is a higher rate of atheism (like me), though that may be simply self-selection of rationalist-minded people rather then de-conversion of religious people.

I personally know a few highly religious biologists (christian as well as muslim) who are quite capable scientists. One high profile biologist springs to mind; defender of evolution and devout catholic Ken Miller. Ultimately the worst conflicts arises between fundamentalist, dogmatic religion and science, with relatively moderate religious brands doing a good job of supporting lots of science, such as through funding research institutions.

Much like people, I believe that how friendly a cat (or dog) is towards humans is largely based on how it was treated as a youngster. Abuse or neglect early on will obviously be a major negative factor in future friendliness

Well, strictly speaking you don't need to study formally to be a conservationist. Wherever you are, it is likely that groups near you will be looking for volunteers for all manner of projects. Here in New Zealand (where I am) theses groups might be non-profit NGOs, run by regional councils or national government.

But exactly what you want to do will determine what you study. For example, if you want to study the animals/plants/ecosystems then an academic research degree is a must. But all I can really say is that you need to talk to a career councilor locally to see about what opportunities are out there and how to best go about getting them.

Regarding the world of conservation, I'm afraid that it is like most science, in that it is cronically underfunded, but full of dedicated people putting out some of the most important science in the world. A very important job, in my opinion:)

When you consider that the average human lifespan was somewhere around 30-40, having children at 15 doesn't seem like such a stretch. Also, life was probably lived in small groups, where child rearing was a cooperative effort, putting less stress on young, inexperienced parents.

This is true to some extent, we take up new material (ie by eating and breathing) and discard old (by excretion of various kinds), making new molecules out of "new" atoms and incorporating them into our bodies. Teeth do change slowly, they can repair themselves to a limited degree, but this so-called turnover of atoms is based on an average rate. Obviously different organs renew themselves at different rates; skin grows constantly, whereas your nervous system has much lower rates of growth.

You can remain the same person during this process for a couple of main reasons. First, each atom of, say, hydrogen is indistinguishable for any other hydrogen atom. Just because it is currently part of a molecule (like water) and is in your body doesn't make it "yours". Your physiology would be perfectly happy with any other hydrogen atom, and that goes for all other atoms (not including radioactive isotopes!!). Secondly, living things can be thought of as an emergent property of organic chemistry. What that means is that you will not find a particular cell, molecule or atom which makes you into you; instead, from the whole process of interacting chemicals, cells and organs emerges the organism which is you. This includes things like personality, which is itself an emergent property of brain function. Damaged sections of your brain can even be compensated for by other sections to some degree. So, even if you exchange lots of "your" atoms with "fresh" atoms you remain the same person because "You" are emergent from the function of interactions and dynamics of those atoms, molecules and cells, not dependant on a particular individual atom or cell being in a particular position.

An emergent phenomenon is defined as a property which cannot be predicted in a complex system by examining parts of that system. You can only detect it by allowing the system to "run" and examining the output.

Have a read here for more information on emergent phenomena.

Not a simple question, it depends entirely on the disease. Some genetic disorders prevent successful breeding, even if the disorder is treated. There is also the matter of carriers who know they are carriers choosing carefully whether or not to have children. Additionally, once selection pressures are removed by a "cure" and the trait becomes effectively neutral, it would still be subjected to drift, which can substatially change allele frequencies over time without specific selection for or against.

Harvey-Weinberg models are useful, but they have certain assumptions which don't really apply to humans, such as random mating and no cross-generational mating. Also, it assumes that genetic traits always follow independent (Mendelian) sorting, which is definitely not the case, and that within the population there is no mutation or migration. Violations of these assumptions result in unexpected outcomes.

Finally, I would consider that an actual "cure" for a genetic disease would necessarily include the correction of the genetic defect, not just treatment or even elimination of symptoms, so the situation you describe wouldn't ever arise.

(posted in Mammals)

Certainly sounds like a mouse to me! They can jump, and are also incredible climbers, capable of moving very quickly up rough surfaces, like a wooden fence.

(posted in Plants & Fungi)

Hi Safir,

Looking for active natural compounds is a wide and ongoing research area. A friend of mine did her master's degree in a chemistry lab which specialised in looking for natural products from Kiwifruit.

The term you are looking for is bioprospecting, which simply means screening plants, animals and microorganisms for interesting and useful compounds.


To some extent this is replaced, or complemented, by artificial combinatorial chemistry which generates new chemicals without having to find them in a natural setting. Combinatorial chemistry is commonly used in research into finding drugs for specific targets.


Of course, when looking at a multiple sequence alignment, some regions of DNA might appear to be protected, others not so, as determined by conservation across individuals or species. This is an illusion caused by selection, which eliminates mutations (ie, individuals with that mutation) that are negative, largely ignores neutral mutations and promotes survival of beneficial mutations. This can lead to regions which appear "protected" and others which do not, but like David says, mutations really are random and can occur at any point in a genome.

If I understand what you are saying correctly, the experiment is precisely re-creating evolution that has happened already, so yes, the outcome would be as identical as the treatment. In effect you are replacing the "environment" part of the adaptation equation with entirely artificial, but apparently identical pressures created in a lab.

Of course, it is impossible to do this because we can't possibly know all of the mutations, AND all of the environmental conditions that have occured for all organisms for all time, not to mention epigenetic changes as well as chance events that have shaped life on earth. In a general sense, evolution is veiwed as a stochastic process; that is, one governed by probability, not certainty. This has lead to the view that if evolution were to proceed again from the beginning, a different set of chance events would occur than during the first time around, resulting in differnt outcomes. One of the many extinction events, for example, might not have happened, especially when the cause is extra-terrestrial like a meteorite strike.

Big cats hunt in different ways. For example, lions hunt as a group using a stalk-and-rush method. Other cats are ambush predators, like jaguar, who wait for the prey to get close then jump them. So yes, domestic cats do basically take small animals in similar ways that their big cousins do, but there is no one particular way that cats hunt.

Chameleons change colour mainly for the purposes of display, for mating, warning off rivals or territorial display, and the colors also do respond to the mood of the animal. I understand that a calm chameleon is usually green. Camouflage is thought to be a secondary purpose, definitely based on local environment colors.

Have a look at this video, which shows a chameleon clearly responding to environmental color.


OK, so the video posted here is actually a fake done as advertising.

When used in chemistry, a moiety is a general term for a part or segment of a molecule. Presumably, a targeting moiety is a chemical signal that targets a larger molecule or complex to a particular area or tissue. I couldn't be more specific without a few more details.

have a look here


Your question is a little confused. Evolution occurs in a population when gene frequencies change over generations. Sometimes new alleles are generated by mutation, which can then be selected for or against. The accumulation of mutations (or possibly epigenetic changes) through selection is adaptation, otherwise known as evolution.